What motor are you using? Stock Flathead or something else? I put a GM HT383 in my '51 F1, and still used the stock battery location. I used rams horn exhaust manifolds. The Toyota PS unit was more of a problem than the battery holder.
Optima makes a very compact 6V battery that can be mounted in any position, even upside down. If you are running 12V you can wire 2 in series. Could be mounted side by side behind or under the seat, laying down under the running board or under the bed, or one behind each headlight panel.